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FORKS: Finding Orderings Robustly using k-means and Steiner trees

https://doi.org/10.1101/132811
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Principal Component Analysis
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Computational methods for trajectory inference from single‐cell transcriptomics
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Multidimensional Scaling by Optimizing Goodness of Fit to a Nonmetric Hypothesis
inferredcites →https://doi.org/10.1007/bfb0020217openalex-snapshot
Kernel principal component analysis
inferredcites →https://doi.org/10.1007/s10994-006-6226-1openalex-snapshot
Extremely randomized trees
inferredcites →https://doi.org/10.1016/0377-0427(87)90125-7openalex-snapshot
Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
inferredcites →https://doi.org/10.1016/j.acha.2006.04.006openalex-snapshot
Diffusion maps
inferredcites →https://doi.org/10.1016/j.cell.2015.04.044openalex-snapshot
Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2015.11.013openalex-snapshot
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
inferredcites →https://doi.org/10.1016/j.cell.2016.03.023openalex-snapshot
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
inferredcites →https://doi.org/10.1016/j.devcel.2010.02.012openalex-snapshot
Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst
inferredcites →https://doi.org/10.1016/j.molcel.2015.04.005openalex-snapshot
The Technology and Biology of Single-Cell RNA Sequencing
inferredcites →https://doi.org/10.1016/j.stem.2015.07.013openalex-snapshot
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis
inferredcites →https://doi.org/10.1016/s0031-3203(03)00084-0openalex-snapshot
Spectral embedding of graphs
inferredcites →https://doi.org/10.1038/nature12172openalex-snapshot
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
inferredcites →https://doi.org/10.1038/nature13173openalex-snapshot
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
inferredcites →https://doi.org/10.1038/nature13437openalex-snapshot
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
inferredcites →https://doi.org/10.1038/nature14966openalex-snapshot
Single-cell messenger RNA sequencing reveals rare intestinal cell types
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/nbt.3154openalex-snapshot
Decoding the regulatory network of early blood development from single-cell gene expression measurements
inferredcites →https://doi.org/10.1038/nbt.3569openalex-snapshot
Wishbone identifies bifurcating developmental trajectories from single-cell data
inferredcites →https://doi.org/10.1038/ncomms11988openalex-snapshot
Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development
inferredcites →https://doi.org/10.1038/ni.2842openalex-snapshot
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses
inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot
Diffusion pseudotime robustly reconstructs lineage branching
inferredcites →https://doi.org/10.1038/nrg3833openalex-snapshot
Computational and analytical challenges in single-cell transcriptomics
inferredcites →https://doi.org/10.1038/nsmb.2660openalex-snapshot
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
inferredcites →https://doi.org/10.1073/pnas.1408993111openalex-snapshot
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.185openalex-snapshot
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
inferredcites →https://doi.org/10.1093/bioinformatics/btv325openalex-snapshot
Diffusion maps for high-dimensional single-cell analysis of differentiation data
inferredcites →https://doi.org/10.1093/bioinformatics/btw372openalex-snapshot
Pseudotime estimation: deconfounding single cell time series
inferredcites →https://doi.org/10.1093/nar/gkv711openalex-snapshot
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
inferredcites →https://doi.org/10.1093/nar/gkw430openalex-snapshot
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
inferredcites →https://doi.org/10.1101/027219openalex-snapshot
Laplacian eigenmaps and principal curves for high resolution pseudotemporal ordering of single-cell RNA-seq profiles
inferredcites →https://doi.org/10.1101/049734openalex-snapshot
Fast, scalable and accurate differential expression analysis for single cells
inferredcites →https://doi.org/10.1101/074971openalex-snapshot
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4 + T cell fate bifurcation
inferredcites →https://doi.org/10.1101/gr.190595.115openalex-snapshot
Defining cell types and states with single-cell genomics
inferredcites →https://doi.org/10.1105/tpc.112.102046openalex-snapshot
Arabidopsis Defense against Botrytis cinerea : Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
inferredcites →https://doi.org/10.1109/34.868688openalex-snapshot
Normalized cuts and image segmentation
inferredcites →https://doi.org/10.1109/mcse.2011.37openalex-snapshot
The NumPy Array: A Structure for Efficient Numerical Computation
inferredcites →https://doi.org/10.1111/j.1745-3984.2003.tb01108.xopenalex-snapshot
Modern Multidimensional Scaling: Theory and Applications
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1126/science.1179050openalex-snapshot
Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens
inferredcites →https://doi.org/10.1126/science.1245316openalex-snapshot
Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
inferredcites →https://doi.org/10.1126/science.1247651openalex-snapshot
Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types
inferredcites →https://doi.org/10.1126/science.290.5500.2319openalex-snapshot
A Global Geometric Framework for Nonlinear Dimensionality Reduction
inferredcites →https://doi.org/10.1126/science.290.5500.2323openalex-snapshot
Nonlinear Dimensionality Reduction by Locally Linear Embedding
inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
inferredcites →https://doi.org/10.1137/0132072openalex-snapshot
The Complexity of Computing Steiner Minimal Trees
inferredcites →https://doi.org/10.1145/1014052.1014118openalex-snapshot
Kernel k-means
inferredcites →https://doi.org/10.1145/2783258.2783309openalex-snapshot
Dimensionality Reduction Via Graph Structure Learning
inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
inferredcites →https://doi.org/10.1186/s13059-016-0927-yopenalex-snapshot
Design and computational analysis of single-cell RNA-sequencing experiments
inferredcites →https://doi.org/10.1186/s13059-016-0975-3openalex-snapshot
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
inferredcites →https://doi.org/10.2307/1412159openalex-snapshot
The Proof and Measurement of Association between Two Things
inferredcites →https://doi.org/10.25080/majora-92bf1922-00aopenalex-snapshot
Data Structures for Statistical Computing in Python
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.7551/mitpress/1120.003.0080openalex-snapshot
Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cyto.a.23976openalex-snapshot
Learning Pathway Dynamics from Single‐Cell Proteomic Data: A Comparative Study
inferred← citeshttps://doi.org/10.1016/j.inffus.2025.103108openalex-snapshot
A Review of BioTree Construction in the Context of Information Fusion: Priors, Methods, Applications and Trends
inferred← citeshttps://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferred← citeshttps://doi.org/10.1093/bfgp/elx029openalex-snapshot
The Human Cell Atlas: Technical approaches and challenges
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